1 Introduction

This paper contains estimates for the effective reproduction number \(R_{t,m}\) over time \(t\) in various nations and other regions \(m\) of United Kingdom. This is done using the methodology as described in [1]. These have been implemented in R using EpiEstim package [2] which is what is used here. The methodolgy and assumptions are described in more detail here.

This paper and it’s results should be updated roughly daily and is available online.

As this paper is updated over time this section will summarise significant changes. The code producing this paper is tracked using Git. The Git commit hash for this project at the time of generating this paper was 2f23b49bb3138389fe9999536f79069c223283c5.

2 Data

Data is obtained [3]. This contains the daily cases, hospital admissions and deaths for United Kingdom by various geographies. Here the data is accessed by specimen date, admission date and date of death.

Once history is built up an allowance for rate reported cases, admissions and deaths will be made. For now the data is cut-off a week prior to the last case date in the data. All data prior to 1 March 2020 are removed.

3 Methodology

The methodology is described in detail here.

4 Results by Nation

4.1 Cases

Below we plot cumulative case count on a log scale by nation:

Cumulative Cases by Nation

Cumulative Cases by Nation

4.2 Admissions

Below we plot cumulative hospital admissions on a log scale.

Cumulative Admissions by Nation

Cumulative Admissions by Nation

4.3 Deaths

Below we plot the cumulative deaths by nation on a log scale:

Cumulative Deaths by Nation

Cumulative Deaths by Nation

4.4 Current \(R_{t,m}\) estimates by Nation

Below current (last weekly) \(R_{t,m}\) estimates are tabulated.

Estimated Effective Reproduction Number by Nation
Nation Estimate Type Count (Last Week) Week Ending R - Lower CI R - Mean R - Uppper CI
England cases 153,929 2020-11-12 1.1 1.1 1.1
England admissions 10,509 2020-11-12 1.1 1.1 1.2
England deaths 2,269 2020-11-12 1.1 1.1 1.2
Northern Ireland cases 4,022 2020-11-12 0.9 1.0 1.0
Northern Ireland admissions 304 2020-11-12 0.8 0.9 1.0
Northern Ireland deaths 72 2020-11-12 0.8 1.1 1.3
Scotland cases 7,891 2020-11-12 1.0 1.0 1.0
Scotland admissions 520 2020-11-12 0.8 0.9 0.9
Scotland deaths 224 2020-11-12 1.0 1.1 1.2
Wales cases 5,722 2020-11-12 0.8 0.8 0.8
Wales admissions 632 2020-11-12 0.9 1.0 1.1
Wales deaths 172 2020-11-12 1.0 1.2 1.4
Estimated Effective Reproduction Number by Nation

Estimated Effective Reproduction Number by Nation

4.5 Maps of Effective Reproduction Number

Below we plot the current effective reproduction number on maps with boundaries provided by [4].

4.5.1 Cases

4.5.2 Admissions

4.5.3 Deaths

4.6 Graphs over Time

Below we plot results for each nation We filter out weeks where the upper end of confidence interval for \(R_{t,m}\) exceeds 4.

4.6.1 England

4.6.2 Northern Ireland

4.6.3 Scotland

4.6.4 Wales

5 Results by Region

5.1 Cases

Below we plot cumulative case count on a log scale by region:

Cumulative Cases by Region

Cumulative Cases by Region

5.2 Deaths

Below we plot the cumulative deaths by region on a log scale:

Cumulative Deaths by Region

Cumulative Deaths by Region

5.3 Current \(R_{t,m}\) estimates by Region

Below current (last weekly) \(R_{t,m}\) estimates are tabulated.

Estimated Effective Reproduction Number by Region
Region Estimate Type Count (Last Week) Week Ending R - Lower CI R - Mean R - Uppper CI
Northern Ireland cases 4,022 2020-11-12 0.9 1.0 1.0
Northern Ireland deaths 72 2020-11-12 0.8 1.1 1.3
Scotland cases 7,891 2020-11-12 1.0 1.0 1.0
Scotland deaths 224 2020-11-12 1.0 1.1 1.2
Wales cases 5,722 2020-11-12 0.8 0.8 0.8
Wales deaths 172 2020-11-12 1.0 1.2 1.4
East Midlands cases 16,491 2020-11-12 1.1 1.1 1.1
East Midlands deaths 254 2020-11-12 1.0 1.1 1.3
East of England cases 9,401 2020-11-12 1.2 1.2 1.3
East of England deaths 127 2020-11-12 0.9 1.1 1.3
London cases 16,963 2020-11-12 1.1 1.2 1.2
London deaths 120 2020-11-12 0.9 1.1 1.3
North East cases 11,315 2020-11-12 1.1 1.2 1.2
North East deaths 164 2020-11-12 0.9 1.1 1.3
North West cases 25,622 2020-11-12 0.9 0.9 0.9
North West deaths 585 2020-11-12 0.9 1.0 1.1
South East cases 16,452 2020-11-12 1.2 1.2 1.3
South East deaths 165 2020-11-12 1.1 1.2 1.4
South West cases 10,679 2020-11-12 1.1 1.1 1.1
South West deaths 103 2020-11-12 1.1 1.3 1.6
West Midlands cases 21,572 2020-11-12 1.1 1.1 1.2
West Midlands deaths 282 2020-11-12 1.0 1.2 1.3
Yorkshire and The Humber cases 24,507 2020-11-12 1.0 1.0 1.0
Yorkshire and The Humber deaths 429 2020-11-12 1.0 1.1 1.2
Estimated Effective Reproduction Number by Region

Estimated Effective Reproduction Number by Region

5.4 Maps of Effective Reproduction Number

Below we plot the current effective reproduction number on maps with boundaries provided by [5].

5.4.1 Cases

5.4.2 Deaths

5.5 Graphs over Time

Below we plot results for each nation We filter out weeks where the upper end of confidence interval for \(R_{t,m}\) exceeds 4.

5.5.1 Northern Ireland

5.5.2 Scotland

5.5.3 Wales

5.5.4 East Midlands

5.5.5 East of England

5.5.6 London

5.5.7 North East

5.5.8 North West

5.5.9 South East

5.5.10 South West

5.5.11 West Midlands

5.5.12 Yorkshire and The Humber

6 Results by NHS Region

6.1 Current \(R_{t,m}\) estimates by Region

Below current (last weekly) \(R_{t,m}\) estimates are tabulated.

Estimated Effective Reproduction Number by Region
Region Estimate Type Count (Last Week) Week Ending R - Lower CI R - Mean R - Uppper CI
Northern Ireland admissions 304 2020-11-12 0.8 0.9 1.0
Scotland admissions 520 2020-11-12 0.8 0.9 0.9
Wales admissions 632 2020-11-12 0.9 1.0 1.1
East of England admissions 624 2020-11-12 1.2 1.3 1.4
London admissions 929 2020-11-12 1.0 1.1 1.1
North West admissions 1,939 2020-11-12 0.9 1.0 1.0
South East admissions 971 2020-11-12 1.2 1.3 1.4
South West admissions 817 2020-11-12 1.1 1.2 1.3
Midlands admissions 2,535 2020-11-12 1.2 1.2 1.3
North East and Yorkshire admissions 2,694 2020-11-12 1.1 1.1 1.1
Estimated Effective Reproduction Number by Region

Estimated Effective Reproduction Number by Region

6.2 Maps of Effective Reproduction Number

Below we plot the current effective reproduction number on maps with boundaries provided by [6].

6.3 Graphs over Time

Below we plot results for each nation We filter out weeks where the upper end of confidence interval for \(R_{t,m}\) exceeds 4.

6.3.1 East of England

6.3.2 London

6.3.3 Midlands

6.3.4 North East and Yorkshire

6.3.5 North West

6.3.6 South East

6.3.7 South West

7 Results by Upper Tier Local Authority

7.1 Highest \(R_{t,m}\) as estimated using cases

Below we plot Upper Tier Local Authorities with the hghest reproduction numbers (providing they had at least 100 cases):

## Selecting by Rt_ui_95
Estimated Effective Reproduction Number by Upper Tier Local Authority
Upper Tier Local Authority Estimate Type Count (Last Week) Week Ending R - Lower CI R - Mean R - Uppper CI
Aberdeenshire cases 136 2020-11-12 1.3 1.6 1.9
East Sussex cases 574 2020-11-12 1.3 1.5 1.7
Herefordshire, County of cases 315 2020-11-12 1.3 1.5 1.7
Kent cases 3,950 2020-11-12 1.3 1.5 1.6
Cambridgeshire cases 980 2020-11-12 1.3 1.4 1.6
Wokingham cases 269 2020-11-12 1.2 1.4 1.6
Medway cases 788 2020-11-12 1.3 1.4 1.5
Causeway Coast and Glens cases 511 2020-11-12 1.2 1.4 1.5
Slough cases 521 2020-11-12 1.2 1.3 1.5
Greenwich cases 475 2020-11-12 1.2 1.3 1.5
Lincolnshire cases 2,706 2020-11-12 1.2 1.3 1.4
Norfolk cases 1,310 2020-11-12 1.2 1.3 1.4
Southend-on-Sea cases 292 2020-11-12 1.2 1.3 1.5
Waltham Forest cases 633 2020-11-12 1.2 1.3 1.4
Aberdeen City cases 119 2020-11-12 1.1 1.3 1.6
Cornwall and Isles of Scilly cases 489 2020-11-12 1.2 1.3 1.4
Hartlepool cases 545 2020-11-12 1.2 1.3 1.4
Kingston upon Thames cases 336 2020-11-12 1.2 1.3 1.4
Bexley cases 675 2020-11-12 1.2 1.3 1.4
Islington cases 426 2020-11-12 1.2 1.3 1.4
Wandsworth cases 605 2020-11-12 1.2 1.3 1.4
Barnet cases 752 2020-11-12 1.2 1.3 1.4
Milton Keynes cases 438 2020-11-12 1.2 1.3 1.4
Kensington and Chelsea cases 232 2020-11-12 1.1 1.2 1.4
Fermanagh and Omagh cases 219 2020-11-12 1.1 1.2 1.4

7.2 Map of Effective Reproduction Number (Cases)

Below we plot the current effective reproduction number estimated from case data on maps with boundaries provided by [7].

7.3 Map over by week since start of the year (experimental)

Below the reproduction number by week for each Upper Tier Local Authority is animated:

8 Detailed Results

Detailed output are saved to a comma-separated value file. The file can be found here.

9 Discussion

Limitation of this method to estimate \(R_{t,m}\) are noted in [1]

  • It’s sensitive to changes in transmissibility, changes in contact patterns, depletion of the susceptible population and control measures.
  • It relies on an assumed generation interval assumptions.
  • The size of the time window can affect the volatility of results.
  • Results are time lagged with regards to true infection, more so in the case of the use of deaths.
  • It’s sensitive to changes in case (or death) detection.
  • The generation interval may change over time.

Further to the above the estimates are made under assumption that the cases and deaths are reported consistently over time. For cases this means that testing needs to be at similar levels and reported with similar lag. Should these change rapidly over an interval of a few weeks the above estimates of the effective reproduction numbers would be biased. For example a rapid expansion of testing over the last 3 weeks would results in overestimating recent effective reproduction numbers. Similarly any changes in reporting (over time and underreporting) of deaths would also bias estimates of the reproduction number estimated using deaths. It may well be that some catch-up in reported deaths is exaggerating the estimates for October.

Estimates for the reproduction number are plotted in time period in which the relevant measure is recorded. Though in reality the infections giving rise to those estimates would have occurred roughly between a week to 4 weeks earlier depending on whether it was cases or deaths. These figures have not been shifted back.

Despite these limitation we believe the ease of calculation of this method and the ability to use multiple sources makes it useful as a monitoring tool.

Having said all the above it would appear that the effective reproduction number was reasonably high in United Kingdom from middle April to middle July. From middle July the figures seems to have decreased well below 1. However since middle September figures have been near 1 and in October these seem to have shifted above 1.

10 Author

This report was prepared by Louis Rossouw. Please get in contact with Louis Rossouw if you have comments or wish to receive this regularly.

Louis Rossouw
Head of Research & Analytics
Gen Re | Life/Health Canada, South Africa, Australia, NZ, UK & Ireland
Email: LRossouw@GenRe.com Mobile: +27 71 355 2550

The views in this document represents that of the author and may not represent those of Gen Re. Also note that given the significant uncertainty involved with the parameters, data and methodology care should be taken with these numbers and any use of these numbers.

11 Digital boundaries

Office for National Statistics licensed under the Open Government Licence v.3.0

Contains OS data © Crown copyright and database right 2020

References

[1] A. Cori, N. M. Ferguson, C. Fraser, and S. Cauchemez, “A new framework and software to estimate time-varying reproduction numbers during epidemics,” American Journal of Epidemiology, vol. 178, no. 9, pp. 1505–1512, Sep. 2013, doi: 10.1093/aje/kwt133. [Online]. Available: https://doi.org/10.1093/aje/kwt133

[2] A. Cori, EpiEstim: A package to estimate time varying reproduction numbers from epidemic curves. 2013 [Online]. Available: https://CRAN.R-project.org/package=EpiEstim

[3] Office for National Statistics, “Official UK Coronavirus Dashboard,” 2020. [Online]. Available: https://coronavirus.data.gov.uk. [Accessed: 07-Nov-2020]

[4] Office for National Statistics, “Countries (December 2019) Boundaries UK BUC,” 09-Oct-2017. [Online]. Available: https://geoportal.statistics.gov.uk/search?collection=Dataset. [Accessed: 07-Nov-2020]

[5] Office for National Statistics, “NUTS Level 1 (January 2018) Ultra Generalised Clipped Boundaries in the United Kingdom,” 31-Jul-2017. [Online]. Available: https://geoportal.statistics.gov.uk/datasets/nuts-level-1-january-2018-ultra-generalised-clipped-boundaries-in-the-united-kingdom. [Accessed: 07-Nov-2020]

[6] Office for National Statistics, “NHS England Regions (April 2020) Boundaries EN BUC,” 13-May-2020. [Online]. Available: https://geoportal.statistics.gov.uk/search?collection=Dataset. [Accessed: 07-Nov-2020]

[7] Office for National Statistics, “Counties and Unitary Authorities (December 2019) Boundaries UK BUC,” 11-Mar-2020. [Online]. Available: https://geoportal.statistics.gov.uk/datasets/counties-and-unitary-authorities-december-2019-boundaries-uk-buc. [Accessed: 07-Nov-2020]